# Submillimetric COVID-19 CT dataset and automatic lung tissue labeling extension

**URL:** <https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007>\
**Category:** Support\
**Tags:** feature, segmentation, data-sets, lung\
**Created:** [February 16, 2021, 10:23am UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007 "2021-02-16T10:23:01Z")\
**Posts on this page:** 14\
**Page:** 1

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**Author:** ![PaoloZaffino](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/paolozaffino/32/81052_2.png) [@PaoloZaffino](https://discourse.slicer.org/u/PaoloZaffino)\
**Post date:** [February 16, 2021, 10:23am UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007/1 "2021-02-16T10:23:01Z")

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Hi all,  
I apologize if I’m posting in the wrong section (if so please remove/move this post).

We just released a free (non commercial use) dataset made of 62 submillimetric CT scans of COVID-19 positive patients.  
Automatic lung tissue labeling and human-based clinical score are provided as well.  
Maybe in this difficult historical period, this dataset can be useful for your research.

Here the article:

> **[An Open-Source COVID-19 CT Dataset with Automatic Lung Tissue Classification...](https://www.mdpi.com/2306-5354/8/2/26)**
>
> The coronavirus disease 19 (COVID-19) pandemic is having a dramatic impact on society and healthcare systems. In this complex scenario, lung computerized tomography (CT) may play an important prognostic role. However, datasets released so far present...

My 2 cents.

Paolo

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**Author:** ![Justin](https://avatars.discourse-cdn.com/v4/letter/j/3ab097/32.png) [@Justin](https://discourse.slicer.org/u/Justin)\
**Post date:** [February 19, 2021, 2:59pm UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007/2 "2021-02-19T14:59:58Z")

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Dear Paolo,

That is great, thanks for your contribution.

Are there other clinical data such as survival outcomes, ICU admission or other (anonymized) data available as well?

Best,  
Justin

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [February 19, 2021, 7:39pm UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007/3 "2021-02-19T19:39:31Z")

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Hi Paolo,

Thank you, this looks like an amazing source.

We recently developed a Lung CT Analyzer extension for 3D Slicer for COVID-19 assessments. It can be installed within Slicer from the extension manager.

The sources can be pull from here: [GitHub - rbumm/SlicerLungCTAnalyzer: This is a 3D Slicer extension for segmentation and spatial reconstruction of infiltrated, collapsed, and emphysematous areas in chest CT examinations.](https://github.com/rbumm/SlicerLungCTAnalyzer)

We will definitely check out your data, comments and ideas for the extension are always welcome !

Best regards

Rudolf Bumm, Chur, Switzerland

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**Author:** ![PaoloZaffino](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/paolozaffino/32/81052_2.png) [@PaoloZaffino](https://discourse.slicer.org/u/PaoloZaffino)\
**Post date:** [February 22, 2021, 11:12am UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007/4 "2021-02-22T11:12:01Z")

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Thanks @Justin !  
We are trying to retrive these data, but I can not promise anything.

@rbumm I saw your extension…that’s really great!  
The aim of our paper was to release high quality images (on internet a lot of people published png-like images…) alongside with some clinical data and a way to automatically get some labels from CTs.  
Let me know if I can provide additional information (as already said we are trying to retrive additional clinical information).

Best,  
Paolo

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [February 22, 2021, 2:37pm UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007/5 "2021-02-22T14:37:27Z")

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I would be very interested in how the community could help to enlarge the dataset.

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**Author:** ![PaoloZaffino](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/paolozaffino/32/81052_2.png) [@PaoloZaffino](https://discourse.slicer.org/u/PaoloZaffino)\
**Post date:** [August 30, 2021, 8:46pm UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007/6 "2021-08-30T20:46:44Z")

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@lassoan @jcfr do you think it would be interesting for the community to have an extension that, given a chest CT, automatically labels lungs tissues on basis of the intensity (healthy, ground-glass opacities, and consolidation)?  
It can be used for pneumonia (COVID too).  
The methodology is explained in the paper linked in the first post (it’s a GMM strategy basically).

We could call it “Lung density segmentation”.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [August 30, 2021, 11:47pm UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007/7 "2021-08-30T23:47:13Z")

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Yes, sure, I expect that this would be useful. If you don’t want to create an entire new extension for this then it could be added to the LungCTAnalyzer or ChestImagingPlatform extensions.

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [August 31, 2021, 8:47pm UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007/8 "2021-08-31T20:47:47Z")

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This sounds interesting, the LungCTAnalyzer does that to some extent, and it would be great if you could add ideas or add functionality yourself.

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**Author:** ![PaoloZaffino](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/paolozaffino/32/81052_2.png) [@PaoloZaffino](https://discourse.slicer.org/u/PaoloZaffino)\
**Post date:** [September 1, 2021, 9:15am UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007/9 "2021-09-01T09:15:06Z")

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I submitted a pull request.

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [September 7, 2021, 10:05am UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007/10 "2021-09-07T10:05:36Z")

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I added a python script

> <https://github.com/rbumm/SlicerLungCTAnalyzer/blob/master/PythonScripts/processAllCTInDir.py>

on the LungCTAnalyzer GitHub that allows analyzing all of your 62 datasets in a row in ~60 minutes (gaming laptop).

As a prerequisite, lung masks have to be prepared once for every CT.

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [September 7, 2021, 11:40am UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007/11 "2021-09-07T11:40:39Z")

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My results of the initial CT’s of all 50 cases are summarized in this google spreadsheet:

> **[LCTA on Submillimetric COVID-19 dataset by PaoloZaffino](https://docs.google.com/spreadsheets/d/1cuZdf1r9Lel4Az3787syDSvQ-C9igWDElcVOhbDjIco/edit?usp=sharing)**
>
> Tabellenblatt1
> 
> clinical score,scanner,sex,user1,user2,user3,func+aff ml,inflated ml,inflated %,emphysema ml,emphysema %,infiltrated ml,infiltrated %,collapsed ml,collapsed %,affected ml,affected %,right func+aff ml,right inflated ml,right inflated...

Thresholds:  
logic.setDefaultThresholds(-1050,-990,-650,-400,0,3000)

Without knowing any clinical details on the patients, LTCA predicts a severe clinical course (20-50% affected lung) in

D:/Patients5\45\CT.nrrd  
D:/Patients5\46\CT.nrrd  
D:/Patients5\7\CT.nrrd  
D:/Patients\35\CT.nrrd  
D:/Patients\33\CT.nrrd  
D:/Patients\15\CT.nrrd  
D:/Patients5\47\CT.nrrd  
D:/Patients\40\CT.nrrd  
D:/Patients\37\CT.nrrd  
D:/Patients\3\CT.nrrd  
D:/Patients\4\CT.nrrd  
D:/Patients\12\CT.nrrd  
D:/Patients\29\CT.nrrd

and a fatal one (\> 50 % affected lung) in

D:/Patients\10\CT.nrrd  
D:/Patients\14\CT.nrrd

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<div class="post-metadata">

**Author:** ![PaoloZaffino](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/paolozaffino/32/81052_2.png) [@PaoloZaffino](https://discourse.slicer.org/u/PaoloZaffino)\
**Post date:** [September 15, 2021, 12:31pm UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007/12 "2021-09-15T12:31:51Z")

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Dear all,  
today I updated our [COVID-19 database](https://www.imagenglab.com/newsite/covid-19/).  
Now it is made of 81 patients (in total 93 CTs since some patients have follow-up scan) and information about intensive care unit were added as well.

@rbumm @Justin

HTH,  
Paolo.

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [September 20, 2021, 12:38pm UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007/13 "2021-09-20T12:38:01Z")

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Very interesting @PaoloZaffino - would it be possible to add mortality data too?  
Thank you  
Best regards  
Rudolf

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**Author:** ![PaoloZaffino](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/paolozaffino/32/81052_2.png) [@PaoloZaffino](https://discourse.slicer.org/u/PaoloZaffino)\
**Post date:** [September 20, 2021, 2:51pm UTC](https://discourse.slicer.org/t/submillimetric-covid-19-ct-dataset-and-automatic-lung-tissue-labeling-extension/16007/14 "2021-09-20T14:51:01Z")

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Not easy to get, but I’ll do my best.

Paolo